Canis familiaris, the domestic dog, is a single species divided into more than 400 phenotypically divergent genetic isolates termed breeds, 152 of which are recognized by the American Kennel Club in the United States (American Kennel Club (1998) The Complete Dog Book, eds. Crowley & Adelman, Howell Book Hues, New York, N.Y.). Distinct breeds of dog are characterized by unique constellations of morphology, behavior, and disease susceptibility (Ostrander et al. (2000) Trends in Genetics 16:117-23). A variety of dog morphologies have existed for millennia, and reproductive isolation between them was formalized with the advent of breed clubs and breed standards in the mid 19th century. Since that time, the promulgation of the “breed barrier” rule—no dog may become a registered member of a breed unless both its dam and sire are registered members—has ensured a relatively closed genetic pool among dogs of each breed.
Over 350 inherited disorders segregate in the purebred dog population (Patterson et al. (1988) J. Am. Vet. Med. Assoc. 193:1131.) Many of these mimic common human disorders and are restricted to particular breeds or groups of breeds as a result of aggressive inbreeding programs used to generate specific morphologies.
There are many potential uses for objectively determining the breed of an individual dog, such as the certification of dogs as belonging to a particular breed. Because historical records vary in reliability from breed to breed, a genetic analysis that does not rely on prior population information is the most direct and accurate method for determining population structure. Over the past decade, molecular methods have been used to enhance our understanding of wild canid species and to determine their relationships to the domestic dog. Mitochondrial DNA sequence analyses describe the relationship between the domestic dog and the wolf, elucidating the multiple domestication events that occurred 40,000-100,000 years ago (Vila et al. (1997) Science 276:1687-9; Savolainen et al. (2002) Science 298:1610-3, Leonard et al. (2002) Science 298:1613-6). However, the evolution of mitochondrial DNA is too slow to allow inference of relationships among modern dog breeds, most of which have existed for fewer than 400 years. In addition, phylogenetic distances measures and tree building programs are not equipped to deal with reticulate evolution as is commonly observed in dog populations (Zajc et al. (1997) Mamm. Genome 8(3):182-5; Koskinen & Bredbacka (2000) Animal Genetics 31:310-17; Irion et al. (2003) J. Hered. 94(1):81-7). One previous study showed that nuclear microsatellite loci could be used to assign dogs from five breeds to their breed of origin, demonstrating large genetic distances among these breeds (Koskinen (2003) Anim. Genet. 34:297). Another study used microsatellites to detect relatedness of two breed pairs in a collection of 28 breeds but could not establish broader phylogenetic relationships among the breeds (Irion et al. (2003) J. Hered 94:81-7). The failure to find such relationships could reflect the properties of microsatellite loci (Irion et al. (2003) J. Hered. 94:81-7), the limited number of breeds examined, or the analytical methods used in the study. Alternatively, it may reflect the complex structure in purebred dog populations, due to the recent origin of most breeds and the mixing of ancestral types in their creation.
There is a need for methods for defining related groups of breeds and for unambiguously identifying breed contributions to the genome of an individual dog. The present invention addresses this and other needs.